Comparative genomics is a powerful tool for uncovering patterns of mutations within genes targeted in human health concerns. To examine structure and function, we sequence targeted genes across multiple species to identify the pattern and rate of substitutions. This report summarizes our completion of projects, current ongoing research, and initiation of new advances with bioinformatic tools used to investigate gene function. In FY 2007-2008, we published novel findings Y chromosome evolution in mamalian species. Sex chromosomes do not evolve the same way as autosomes and the extent of this difference was rigorously evaluated using the 8 species of bear as a model system. X-linked and Y-linked genes also evolve differently due to population history within species. We demonstrate a remarkable sex-linked bias in the wild to prove this concept. We published a complete lack of variation in Y chromosome regions sequenced from large samples of male lions throughout the African continent and proving the incidence of sex bias in population evolution, expansion and contraction. This type of information is essential to interpretation of disease gene mutation, distribution and transmission within populations, including humans. We have completed our project investigating the theory that genes on the X and Y chromosome evolve in very different ways from those on autosomes. We describe differential rates of genetic change between protein-coding and noncoding regions between the X- chromosome, Y-chromosome and autosomes. Our study encompasses nearly 24 kb of data from each of 37 species of cat. This will give us a broad depiction of genome evolution that can assist not only in the study of human disease but how genome evolution occurs across mammals. These data have been presented in international meetings in 2008 and will be published. Our ongoing initiative is the development and implementation of multiple bioinformatic methods to efficiently identify genes, map their position on mammalian X and Y chromosomes, and investigate their evolution and function. We anticipate new insights through the recent incorporation of our whole genome studies of alpaca (artiodactyls), cat and pangolin (carnivore), and our ongoing phylogenetic investigation of over 200 species of primates. Assessment of patterns of change in genes linked with human disease, including cancer, can be accomplished by comparative genomics across species. Currently we are assessing X-Y linked genes in 200 species of primates using sequencing and bioinformatic technologies. Additional tools are being developed to help annotate newly published and released primate Y chromosome sequence.